Multiple sequence alignment - TraesCS5B01G557600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G557600 chr5B 100.000 2501 0 0 1 2501 705321346 705318846 0.000000e+00 4619.0
1 TraesCS5B01G557600 chr5B 78.240 818 144 19 697 1512 705330044 705329259 6.210000e-136 494.0
2 TraesCS5B01G557600 chr5B 93.878 49 1 2 2265 2312 705298925 705298878 3.450000e-09 73.1
3 TraesCS5B01G557600 chr5B 93.878 49 1 2 2265 2312 705307186 705307139 3.450000e-09 73.1
4 TraesCS5B01G557600 chr5B 93.878 49 1 2 2265 2312 705314529 705314482 3.450000e-09 73.1
5 TraesCS5B01G557600 chr5D 89.574 1410 95 17 644 2047 557518940 557520303 0.000000e+00 1742.0
6 TraesCS5B01G557600 chr5D 90.355 985 58 18 60 1024 290837800 290838767 0.000000e+00 1258.0
7 TraesCS5B01G557600 chr5D 96.026 302 10 1 2139 2438 557522699 557523000 8.040000e-135 490.0
8 TraesCS5B01G557600 chr5D 74.937 790 160 25 710 1487 526095820 526095057 6.670000e-86 327.0
9 TraesCS5B01G557600 chr5D 87.117 163 20 1 2230 2391 557523389 557523551 1.530000e-42 183.0
10 TraesCS5B01G557600 chr5D 84.756 164 23 2 2230 2391 557526218 557526381 1.990000e-36 163.0
11 TraesCS5B01G557600 chr4A 92.958 710 46 3 560 1268 609750543 609751249 0.000000e+00 1031.0
12 TraesCS5B01G557600 chr4A 92.670 382 18 4 1478 1849 609789338 609789719 2.190000e-150 542.0
13 TraesCS5B01G557600 chr4A 93.233 133 9 0 1347 1479 609751256 609751388 1.960000e-46 196.0
14 TraesCS5B01G557600 chr4A 97.143 35 0 1 2401 2434 609797553 609797587 9.660000e-05 58.4
15 TraesCS5B01G557600 chr2D 87.817 829 60 17 223 1024 261206833 261207647 0.000000e+00 933.0
16 TraesCS5B01G557600 chr2A 86.877 823 65 25 58 858 28103105 28103906 0.000000e+00 881.0
17 TraesCS5B01G557600 chr2A 85.770 766 65 23 58 800 762079691 762080435 0.000000e+00 771.0
18 TraesCS5B01G557600 chr2A 86.444 450 39 9 109 549 49861805 49861369 8.100000e-130 473.0
19 TraesCS5B01G557600 chr2A 91.781 292 18 4 570 861 675799222 675798937 3.870000e-108 401.0
20 TraesCS5B01G557600 chr2A 84.783 414 41 10 109 513 239399754 239400154 1.800000e-106 396.0
21 TraesCS5B01G557600 chr2A 91.349 289 19 4 570 858 46037803 46038085 8.390000e-105 390.0
22 TraesCS5B01G557600 chr3A 86.364 770 65 21 109 858 727326090 727326839 0.000000e+00 804.0
23 TraesCS5B01G557600 chr6B 86.107 763 67 23 58 800 310605867 310605124 0.000000e+00 785.0
24 TraesCS5B01G557600 chr2B 85.901 766 64 23 58 800 795317692 795316948 0.000000e+00 776.0
25 TraesCS5B01G557600 chr5A 85.436 769 74 19 109 858 13166223 13166972 0.000000e+00 765.0
26 TraesCS5B01G557600 chr5A 91.349 289 19 4 570 858 344831875 344832157 8.390000e-105 390.0
27 TraesCS5B01G557600 chr7A 85.333 450 44 9 109 549 55250010 55249574 1.760000e-121 446.0
28 TraesCS5B01G557600 chr7A 91.696 289 18 4 570 858 133559596 133559878 1.800000e-106 396.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G557600 chr5B 705318846 705321346 2500 True 4619.0 4619 100.00000 1 2501 1 chr5B.!!$R4 2500
1 TraesCS5B01G557600 chr5B 705329259 705330044 785 True 494.0 494 78.24000 697 1512 1 chr5B.!!$R5 815
2 TraesCS5B01G557600 chr5D 290837800 290838767 967 False 1258.0 1258 90.35500 60 1024 1 chr5D.!!$F1 964
3 TraesCS5B01G557600 chr5D 557518940 557526381 7441 False 644.5 1742 89.36825 644 2438 4 chr5D.!!$F2 1794
4 TraesCS5B01G557600 chr5D 526095057 526095820 763 True 327.0 327 74.93700 710 1487 1 chr5D.!!$R1 777
5 TraesCS5B01G557600 chr4A 609750543 609751388 845 False 613.5 1031 93.09550 560 1479 2 chr4A.!!$F3 919
6 TraesCS5B01G557600 chr2D 261206833 261207647 814 False 933.0 933 87.81700 223 1024 1 chr2D.!!$F1 801
7 TraesCS5B01G557600 chr2A 28103105 28103906 801 False 881.0 881 86.87700 58 858 1 chr2A.!!$F1 800
8 TraesCS5B01G557600 chr2A 762079691 762080435 744 False 771.0 771 85.77000 58 800 1 chr2A.!!$F4 742
9 TraesCS5B01G557600 chr3A 727326090 727326839 749 False 804.0 804 86.36400 109 858 1 chr3A.!!$F1 749
10 TraesCS5B01G557600 chr6B 310605124 310605867 743 True 785.0 785 86.10700 58 800 1 chr6B.!!$R1 742
11 TraesCS5B01G557600 chr2B 795316948 795317692 744 True 776.0 776 85.90100 58 800 1 chr2B.!!$R1 742
12 TraesCS5B01G557600 chr5A 13166223 13166972 749 False 765.0 765 85.43600 109 858 1 chr5A.!!$F1 749

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
43 44 0.174617 CTCTCCTTCAGCCTCCGTTC 59.825 60.0 0.00 0.0 0.00 3.95 F
1310 1350 0.318784 GTCAGGGACGACAGTGACAC 60.319 60.0 11.88 0.0 39.33 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1353 0.033504 GGTGGTGTCACTGTCGTCAT 59.966 55.000 2.35 0.0 43.17 3.06 R
2212 4640 3.162666 TCGGTCTCTCAACATAACCAGT 58.837 45.455 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.179599 CTCCTCCCTCCCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
31 32 2.041928 CCCCCTCAGCCTCTCCTT 59.958 66.667 0.00 0.00 0.00 3.36
32 33 2.069430 CCCCCTCAGCCTCTCCTTC 61.069 68.421 0.00 0.00 0.00 3.46
33 34 1.306482 CCCCTCAGCCTCTCCTTCA 60.306 63.158 0.00 0.00 0.00 3.02
34 35 1.336632 CCCCTCAGCCTCTCCTTCAG 61.337 65.000 0.00 0.00 0.00 3.02
35 36 1.521616 CCTCAGCCTCTCCTTCAGC 59.478 63.158 0.00 0.00 0.00 4.26
36 37 1.521616 CTCAGCCTCTCCTTCAGCC 59.478 63.158 0.00 0.00 0.00 4.85
37 38 0.977108 CTCAGCCTCTCCTTCAGCCT 60.977 60.000 0.00 0.00 0.00 4.58
38 39 0.975040 TCAGCCTCTCCTTCAGCCTC 60.975 60.000 0.00 0.00 0.00 4.70
39 40 1.688884 AGCCTCTCCTTCAGCCTCC 60.689 63.158 0.00 0.00 0.00 4.30
40 41 3.087666 GCCTCTCCTTCAGCCTCCG 62.088 68.421 0.00 0.00 0.00 4.63
41 42 1.684049 CCTCTCCTTCAGCCTCCGT 60.684 63.158 0.00 0.00 0.00 4.69
42 43 1.261238 CCTCTCCTTCAGCCTCCGTT 61.261 60.000 0.00 0.00 0.00 4.44
43 44 0.174617 CTCTCCTTCAGCCTCCGTTC 59.825 60.000 0.00 0.00 0.00 3.95
44 45 1.219393 CTCCTTCAGCCTCCGTTCC 59.781 63.158 0.00 0.00 0.00 3.62
45 46 2.125512 CCTTCAGCCTCCGTTCCG 60.126 66.667 0.00 0.00 0.00 4.30
46 47 2.815647 CTTCAGCCTCCGTTCCGC 60.816 66.667 0.00 0.00 0.00 5.54
47 48 4.388499 TTCAGCCTCCGTTCCGCC 62.388 66.667 0.00 0.00 0.00 6.13
51 52 4.796495 GCCTCCGTTCCGCCCAAT 62.796 66.667 0.00 0.00 0.00 3.16
52 53 2.045340 CCTCCGTTCCGCCCAATT 60.045 61.111 0.00 0.00 0.00 2.32
53 54 1.677633 CCTCCGTTCCGCCCAATTT 60.678 57.895 0.00 0.00 0.00 1.82
54 55 1.248101 CCTCCGTTCCGCCCAATTTT 61.248 55.000 0.00 0.00 0.00 1.82
55 56 0.601057 CTCCGTTCCGCCCAATTTTT 59.399 50.000 0.00 0.00 0.00 1.94
97 100 2.483877 TGTGAATCGTGATGGTTGCTTC 59.516 45.455 0.00 0.00 0.00 3.86
177 180 2.223340 GGTGTTTGCGATAATGCCTCTG 60.223 50.000 0.00 0.00 0.00 3.35
192 195 2.353109 GCCTCTGGGAAAGTTGAAATGC 60.353 50.000 0.00 0.00 33.58 3.56
210 213 2.768698 TGCCAATTTGTTCAGCCAATG 58.231 42.857 0.00 0.00 0.00 2.82
211 214 2.104451 TGCCAATTTGTTCAGCCAATGT 59.896 40.909 0.00 0.00 0.00 2.71
212 215 3.323115 TGCCAATTTGTTCAGCCAATGTA 59.677 39.130 0.00 0.00 0.00 2.29
229 232 7.653713 AGCCAATGTAGTAGAATTCTATGTTCG 59.346 37.037 17.95 4.81 0.00 3.95
328 333 4.685628 CACAAACAAAACATCTATGGGTGC 59.314 41.667 0.00 0.00 0.00 5.01
384 391 6.260493 AGAAAATGCTCTCATCAGATTAGCAC 59.740 38.462 12.13 3.13 42.13 4.40
385 392 4.684484 ATGCTCTCATCAGATTAGCACA 57.316 40.909 12.13 2.60 42.13 4.57
386 393 4.684484 TGCTCTCATCAGATTAGCACAT 57.316 40.909 7.49 0.00 37.59 3.21
387 394 5.796424 TGCTCTCATCAGATTAGCACATA 57.204 39.130 7.49 0.00 37.59 2.29
388 395 6.356186 TGCTCTCATCAGATTAGCACATAT 57.644 37.500 7.49 0.00 37.59 1.78
389 396 7.472334 TGCTCTCATCAGATTAGCACATATA 57.528 36.000 7.49 0.00 37.59 0.86
409 416 8.605947 ACATATATATAAGGTGTGGTTCATGCT 58.394 33.333 0.00 0.00 0.00 3.79
425 440 3.509967 TCATGCTTCCAAGACGTCTTCTA 59.490 43.478 27.54 15.59 32.51 2.10
430 445 4.564769 GCTTCCAAGACGTCTTCTATTCTG 59.435 45.833 27.54 15.25 32.51 3.02
435 450 6.602009 TCCAAGACGTCTTCTATTCTGTATGA 59.398 38.462 27.54 6.23 32.51 2.15
455 471 4.139786 TGAAGAGAAGCTGACTTGCATTT 58.860 39.130 5.29 0.00 35.82 2.32
462 478 1.466360 GCTGACTTGCATTTACGGCTG 60.466 52.381 0.00 0.00 0.00 4.85
473 489 4.614535 GCATTTACGGCTGATGATGATTCC 60.615 45.833 0.00 0.00 0.00 3.01
476 492 2.843701 ACGGCTGATGATGATTCCTTC 58.156 47.619 0.00 0.00 0.00 3.46
496 512 6.946009 TCCTTCTGTTCCATAGTTTAAAAGGG 59.054 38.462 0.00 0.00 32.34 3.95
527 543 5.895636 TTTGCACTGGATAACCAAGTATG 57.104 39.130 0.00 0.00 46.32 2.39
531 547 4.517285 CACTGGATAACCAAGTATGCTGT 58.483 43.478 0.00 0.00 46.32 4.40
541 557 4.018415 ACCAAGTATGCTGTCAGGGTTAAT 60.018 41.667 1.14 0.00 0.00 1.40
549 565 9.869757 GTATGCTGTCAGGGTTAATTTTAATTT 57.130 29.630 1.14 0.00 0.00 1.82
610 636 6.986231 CCCATTTTATTTCCTTAGGCAATGTC 59.014 38.462 6.40 0.00 0.00 3.06
611 637 6.697019 CCATTTTATTTCCTTAGGCAATGTCG 59.303 38.462 6.40 0.00 0.00 4.35
612 638 6.827586 TTTTATTTCCTTAGGCAATGTCGT 57.172 33.333 6.40 0.00 0.00 4.34
613 639 6.431198 TTTATTTCCTTAGGCAATGTCGTC 57.569 37.500 6.40 0.00 0.00 4.20
726 752 0.819259 GGCCGCCATTGAGCAGAATA 60.819 55.000 3.91 0.00 0.00 1.75
727 753 1.242076 GCCGCCATTGAGCAGAATAT 58.758 50.000 0.00 0.00 0.00 1.28
756 789 2.340078 GCAGTGGCGACAGAGTGA 59.660 61.111 0.00 0.00 44.46 3.41
1168 1208 3.634397 TGGAAATGTCTCTGACCATCC 57.366 47.619 0.00 0.00 32.19 3.51
1292 1332 5.327732 CCCTATATGCATGGAGGATTTTGT 58.672 41.667 23.63 0.00 0.00 2.83
1295 1335 6.150641 CCTATATGCATGGAGGATTTTGTCAG 59.849 42.308 19.27 0.00 0.00 3.51
1296 1336 2.449464 TGCATGGAGGATTTTGTCAGG 58.551 47.619 0.00 0.00 0.00 3.86
1297 1337 1.753073 GCATGGAGGATTTTGTCAGGG 59.247 52.381 0.00 0.00 0.00 4.45
1298 1338 2.621407 GCATGGAGGATTTTGTCAGGGA 60.621 50.000 0.00 0.00 0.00 4.20
1299 1339 2.879103 TGGAGGATTTTGTCAGGGAC 57.121 50.000 0.00 0.00 0.00 4.46
1301 1341 1.278127 GGAGGATTTTGTCAGGGACGA 59.722 52.381 0.00 0.00 34.95 4.20
1302 1342 2.347731 GAGGATTTTGTCAGGGACGAC 58.652 52.381 0.00 0.00 34.95 4.34
1304 1344 2.076863 GGATTTTGTCAGGGACGACAG 58.923 52.381 0.00 0.00 46.14 3.51
1307 1347 1.116308 TTTGTCAGGGACGACAGTGA 58.884 50.000 0.00 0.00 46.14 3.41
1309 1349 0.753848 TGTCAGGGACGACAGTGACA 60.754 55.000 14.37 14.37 45.39 3.58
1310 1350 0.318784 GTCAGGGACGACAGTGACAC 60.319 60.000 11.88 0.00 39.33 3.67
1312 1352 1.456892 AGGGACGACAGTGACACCA 60.457 57.895 0.84 0.00 0.00 4.17
1313 1353 1.046472 AGGGACGACAGTGACACCAA 61.046 55.000 0.84 0.00 0.00 3.67
1314 1354 0.034896 GGGACGACAGTGACACCAAT 59.965 55.000 0.84 0.00 0.00 3.16
1369 1409 1.152030 TGCTCCCACTCCTTCCACT 60.152 57.895 0.00 0.00 0.00 4.00
1373 1413 2.583441 CCCACTCCTTCCACTGCGA 61.583 63.158 0.00 0.00 0.00 5.10
1527 1567 0.744414 ACCCGAAGCATGATGTTCCG 60.744 55.000 0.00 0.00 0.00 4.30
1540 1580 1.358152 TGTTCCGAGGATCAAGGGTT 58.642 50.000 0.00 0.00 33.17 4.11
1599 1639 2.819595 GAATCCTGCAGCCGCGAA 60.820 61.111 8.23 0.00 42.97 4.70
1654 1694 7.724061 TGTAGAGGATGACTTGTATATGCAGTA 59.276 37.037 0.00 0.00 0.00 2.74
1719 1759 5.855045 GGTATCTACCGGTCAATTGAATCT 58.145 41.667 12.40 0.00 36.50 2.40
1766 1806 2.698274 TCTTCTGGACAGCAAGTGTGTA 59.302 45.455 0.00 0.00 40.56 2.90
1767 1807 2.820059 TCTGGACAGCAAGTGTGTAG 57.180 50.000 0.00 0.00 40.56 2.74
1769 1809 3.227614 TCTGGACAGCAAGTGTGTAGTA 58.772 45.455 0.00 0.00 40.56 1.82
1793 1838 4.462483 GGTTTCATTCAGAGGGCAAATACA 59.538 41.667 0.00 0.00 0.00 2.29
1795 1840 6.351286 GGTTTCATTCAGAGGGCAAATACATT 60.351 38.462 0.00 0.00 0.00 2.71
1803 1848 4.229582 AGAGGGCAAATACATTAACCTGGA 59.770 41.667 0.00 0.00 0.00 3.86
1828 1874 0.622665 ATGCTTAGCCAGGCTTCAGT 59.377 50.000 22.26 0.00 40.44 3.41
1831 1877 1.457346 CTTAGCCAGGCTTCAGTTGG 58.543 55.000 22.26 0.00 40.44 3.77
1861 1907 2.124122 GCCTTGTGCTTTTGGTTTACG 58.876 47.619 0.00 0.00 36.87 3.18
1905 1951 5.681337 TGTTTTCGTGCTGTGAAATGATA 57.319 34.783 0.63 0.00 35.43 2.15
1918 1964 9.585099 GCTGTGAAATGATAATTTTGTTATCCA 57.415 29.630 5.60 0.00 31.99 3.41
1955 2006 7.780064 TGTTGTATTTGCCAAATATGCAGTAT 58.220 30.769 12.69 0.00 40.35 2.12
2000 2051 3.755378 GGGTGCAAGCATATATCCTCTTG 59.245 47.826 0.00 11.65 39.00 3.02
2012 2063 9.117183 GCATATATCCTCTTGCATTTCATCATA 57.883 33.333 0.00 0.00 35.22 2.15
2047 2098 3.206090 GCAAGAGCCAAAAAGCAGG 57.794 52.632 0.00 0.00 34.23 4.85
2048 2099 0.390492 GCAAGAGCCAAAAAGCAGGT 59.610 50.000 0.00 0.00 34.23 4.00
2049 2100 1.202568 GCAAGAGCCAAAAAGCAGGTT 60.203 47.619 0.00 0.00 34.23 3.50
2050 2101 2.747436 CAAGAGCCAAAAAGCAGGTTC 58.253 47.619 0.00 0.00 35.60 3.62
2051 2102 2.071778 AGAGCCAAAAAGCAGGTTCA 57.928 45.000 0.00 0.00 37.57 3.18
2052 2103 1.959282 AGAGCCAAAAAGCAGGTTCAG 59.041 47.619 0.00 0.00 37.57 3.02
2053 2104 1.956477 GAGCCAAAAAGCAGGTTCAGA 59.044 47.619 0.00 0.00 35.48 3.27
2054 2105 1.683385 AGCCAAAAAGCAGGTTCAGAC 59.317 47.619 0.00 0.00 34.23 3.51
2055 2106 1.683385 GCCAAAAAGCAGGTTCAGACT 59.317 47.619 0.00 0.00 0.00 3.24
2056 2107 2.544486 GCCAAAAAGCAGGTTCAGACTG 60.544 50.000 0.00 0.00 38.95 3.51
2065 2116 4.462508 CAGGTTCAGACTGCTCTATTGA 57.537 45.455 0.00 0.00 0.00 2.57
2066 2117 5.021033 CAGGTTCAGACTGCTCTATTGAT 57.979 43.478 0.00 0.00 0.00 2.57
2067 2118 5.049167 CAGGTTCAGACTGCTCTATTGATC 58.951 45.833 0.00 0.00 0.00 2.92
2068 2119 4.713814 AGGTTCAGACTGCTCTATTGATCA 59.286 41.667 0.00 0.00 0.00 2.92
2069 2120 5.188555 AGGTTCAGACTGCTCTATTGATCAA 59.811 40.000 11.26 11.26 0.00 2.57
2070 2121 6.054295 GGTTCAGACTGCTCTATTGATCAAT 58.946 40.000 23.75 23.75 34.93 2.57
2071 2122 6.541641 GGTTCAGACTGCTCTATTGATCAATT 59.458 38.462 25.26 6.25 32.50 2.32
2072 2123 7.712639 GGTTCAGACTGCTCTATTGATCAATTA 59.287 37.037 25.26 13.39 32.50 1.40
2073 2124 9.270640 GTTCAGACTGCTCTATTGATCAATTAT 57.729 33.333 25.26 5.76 32.50 1.28
2074 2125 9.842775 TTCAGACTGCTCTATTGATCAATTATT 57.157 29.630 25.26 5.38 32.50 1.40
2106 2157 8.967664 TCAAATACACACCACTAAAAAGTACT 57.032 30.769 0.00 0.00 0.00 2.73
2107 2158 8.832521 TCAAATACACACCACTAAAAAGTACTG 58.167 33.333 0.00 0.00 0.00 2.74
2108 2159 6.796705 ATACACACCACTAAAAAGTACTGC 57.203 37.500 0.00 0.00 0.00 4.40
2109 2160 3.558418 ACACACCACTAAAAAGTACTGCG 59.442 43.478 0.00 0.00 0.00 5.18
2110 2161 3.805422 CACACCACTAAAAAGTACTGCGA 59.195 43.478 0.00 0.00 0.00 5.10
2111 2162 3.805971 ACACCACTAAAAAGTACTGCGAC 59.194 43.478 0.00 0.00 0.00 5.19
2112 2163 4.056050 CACCACTAAAAAGTACTGCGACT 58.944 43.478 0.00 0.00 0.00 4.18
2113 2164 4.510340 CACCACTAAAAAGTACTGCGACTT 59.490 41.667 0.00 0.00 41.50 3.01
2115 2166 5.007332 ACCACTAAAAAGTACTGCGACTTTG 59.993 40.000 10.81 3.59 46.52 2.77
2116 2167 4.904154 CACTAAAAAGTACTGCGACTTTGC 59.096 41.667 10.81 0.00 46.52 3.68
2117 2168 4.814771 ACTAAAAAGTACTGCGACTTTGCT 59.185 37.500 10.81 5.75 46.52 3.91
2123 2174 4.483311 AGTACTGCGACTTTGCTAGTTAC 58.517 43.478 0.00 0.00 37.17 2.50
2183 4611 5.720202 AGCTAAATTATGTGTCGACTGTCA 58.280 37.500 17.92 13.25 0.00 3.58
2212 4640 6.094325 ACGAACTTGGTGTACAGAAATTTGAA 59.906 34.615 0.00 0.00 0.00 2.69
2298 4726 4.607239 AGATCAAAAGCCATGGAGAACAT 58.393 39.130 18.40 0.00 41.57 2.71
2313 4743 4.819088 GGAGAACATCTTTAGCTTCATCCC 59.181 45.833 0.00 0.00 0.00 3.85
2369 4799 2.903284 CACTTTTGTGTGGGCATGC 58.097 52.632 9.90 9.90 44.94 4.06
2376 4806 0.469705 TGTGTGGGCATGCTTCCTTT 60.470 50.000 18.92 0.00 0.00 3.11
2391 4821 8.872845 CATGCTTCCTTTGTTCCAAAATATAAC 58.127 33.333 0.00 0.00 0.00 1.89
2393 4823 7.015682 TGCTTCCTTTGTTCCAAAATATAACCA 59.984 33.333 0.00 0.00 0.00 3.67
2413 4843 4.219725 ACCATGTATAACTTTTGTGTGGGC 59.780 41.667 0.00 0.00 0.00 5.36
2440 4897 5.748630 GCTTCCTTCGTTTCAAAAGTTTGAT 59.251 36.000 7.28 0.00 45.65 2.57
2441 4898 6.074835 GCTTCCTTCGTTTCAAAAGTTTGATC 60.075 38.462 7.28 4.03 45.65 2.92
2442 4899 6.443934 TCCTTCGTTTCAAAAGTTTGATCA 57.556 33.333 7.28 0.00 45.65 2.92
2457 4914 0.526954 GATCAGCCCAAATTGCGCAG 60.527 55.000 11.31 0.00 0.00 5.18
2471 4928 2.084844 CGCAGCTTCATGTGAGGTC 58.915 57.895 0.00 0.00 32.27 3.85
2474 4931 1.741732 GCAGCTTCATGTGAGGTCGAT 60.742 52.381 0.00 0.00 0.00 3.59
2481 4938 5.508825 GCTTCATGTGAGGTCGATTAGATCT 60.509 44.000 0.00 0.00 44.53 2.75
2495 4952 7.273815 GTCGATTAGATCTTTCGATAATCACCC 59.726 40.741 24.45 11.65 43.03 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.179599 GGGGGAGGGAGGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
14 15 2.041928 AAGGAGAGGCTGAGGGGG 59.958 66.667 0.00 0.00 0.00 5.40
15 16 1.306482 TGAAGGAGAGGCTGAGGGG 60.306 63.158 0.00 0.00 0.00 4.79
16 17 1.970352 GCTGAAGGAGAGGCTGAGGG 61.970 65.000 0.00 0.00 0.00 4.30
17 18 1.521616 GCTGAAGGAGAGGCTGAGG 59.478 63.158 0.00 0.00 0.00 3.86
18 19 0.977108 AGGCTGAAGGAGAGGCTGAG 60.977 60.000 0.00 0.00 44.23 3.35
19 20 0.975040 GAGGCTGAAGGAGAGGCTGA 60.975 60.000 0.00 0.00 45.79 4.26
20 21 1.521616 GAGGCTGAAGGAGAGGCTG 59.478 63.158 0.00 0.00 45.79 4.85
22 23 2.907236 GGAGGCTGAAGGAGAGGC 59.093 66.667 0.00 0.00 36.26 4.70
23 24 1.261238 AACGGAGGCTGAAGGAGAGG 61.261 60.000 0.00 0.00 0.00 3.69
24 25 0.174617 GAACGGAGGCTGAAGGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
25 26 1.258445 GGAACGGAGGCTGAAGGAGA 61.258 60.000 0.00 0.00 0.00 3.71
26 27 1.219393 GGAACGGAGGCTGAAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
27 28 3.388841 GGAACGGAGGCTGAAGGA 58.611 61.111 0.00 0.00 0.00 3.36
58 59 0.164217 CAAACGCCACATGCAATTGC 59.836 50.000 23.69 23.69 41.33 3.56
59 60 1.192757 CACAAACGCCACATGCAATTG 59.807 47.619 0.00 0.00 41.33 2.32
60 61 1.068281 TCACAAACGCCACATGCAATT 59.932 42.857 0.00 0.00 41.33 2.32
61 62 0.672889 TCACAAACGCCACATGCAAT 59.327 45.000 0.00 0.00 41.33 3.56
62 63 0.457443 TTCACAAACGCCACATGCAA 59.543 45.000 0.00 0.00 41.33 4.08
63 64 0.672889 ATTCACAAACGCCACATGCA 59.327 45.000 0.00 0.00 41.33 3.96
64 65 1.339711 GATTCACAAACGCCACATGC 58.660 50.000 0.00 0.00 0.00 4.06
114 117 1.788258 CACCTGCGGCATAGACTATG 58.212 55.000 16.80 16.80 39.18 2.23
146 149 2.252260 CAAACACCTTGCGAGCGG 59.748 61.111 0.00 0.00 0.00 5.52
167 170 4.380843 TTCAACTTTCCCAGAGGCATTA 57.619 40.909 0.00 0.00 0.00 1.90
177 180 4.821260 ACAAATTGGCATTTCAACTTTCCC 59.179 37.500 0.00 0.00 29.41 3.97
192 195 5.138125 ACTACATTGGCTGAACAAATTGG 57.862 39.130 0.00 0.00 33.48 3.16
210 213 7.928103 TCCTGTCGAACATAGAATTCTACTAC 58.072 38.462 17.35 7.70 0.00 2.73
211 214 8.693120 ATCCTGTCGAACATAGAATTCTACTA 57.307 34.615 17.35 0.00 0.00 1.82
212 215 7.589958 ATCCTGTCGAACATAGAATTCTACT 57.410 36.000 17.35 5.40 0.00 2.57
229 232 6.492087 GTCCATAGGCTCCTATATATCCTGTC 59.508 46.154 8.04 0.00 37.16 3.51
240 244 4.892198 AGTTTAAGGTCCATAGGCTCCTA 58.108 43.478 0.00 0.00 0.00 2.94
328 333 4.465512 GCGCAGTGCCAACATCCG 62.466 66.667 10.11 0.00 37.76 4.18
384 391 9.453572 AAGCATGAACCACACCTTATATATATG 57.546 33.333 5.44 0.00 0.00 1.78
385 392 9.672673 GAAGCATGAACCACACCTTATATATAT 57.327 33.333 0.00 0.00 0.00 0.86
386 393 8.100791 GGAAGCATGAACCACACCTTATATATA 58.899 37.037 0.00 0.00 0.00 0.86
387 394 6.942576 GGAAGCATGAACCACACCTTATATAT 59.057 38.462 0.00 0.00 0.00 0.86
388 395 6.126623 TGGAAGCATGAACCACACCTTATATA 60.127 38.462 0.00 0.00 0.00 0.86
389 396 5.133221 GGAAGCATGAACCACACCTTATAT 58.867 41.667 0.00 0.00 0.00 0.86
394 401 0.478072 TGGAAGCATGAACCACACCT 59.522 50.000 0.00 0.00 0.00 4.00
401 408 2.417719 AGACGTCTTGGAAGCATGAAC 58.582 47.619 13.58 0.00 0.00 3.18
409 416 5.723672 ACAGAATAGAAGACGTCTTGGAA 57.276 39.130 34.23 18.97 37.84 3.53
425 440 6.543430 AGTCAGCTTCTCTTCATACAGAAT 57.457 37.500 0.00 0.00 35.25 2.40
430 445 4.248859 TGCAAGTCAGCTTCTCTTCATAC 58.751 43.478 0.00 0.00 31.49 2.39
435 450 4.153117 CGTAAATGCAAGTCAGCTTCTCTT 59.847 41.667 0.00 0.00 31.49 2.85
455 471 3.643320 AGAAGGAATCATCATCAGCCGTA 59.357 43.478 0.00 0.00 0.00 4.02
496 512 3.683365 ATCCAGTGCAAAAATGGGTTC 57.317 42.857 8.23 0.00 34.71 3.62
501 517 5.540911 ACTTGGTTATCCAGTGCAAAAATG 58.459 37.500 0.00 0.00 45.22 2.32
502 518 5.806654 ACTTGGTTATCCAGTGCAAAAAT 57.193 34.783 0.00 0.00 45.22 1.82
503 519 6.686630 CATACTTGGTTATCCAGTGCAAAAA 58.313 36.000 0.00 0.00 45.22 1.94
561 577 7.340999 GGGCAAAAGGAGGAGTGTATAAATTAA 59.659 37.037 0.00 0.00 0.00 1.40
564 580 5.201243 GGGCAAAAGGAGGAGTGTATAAAT 58.799 41.667 0.00 0.00 0.00 1.40
565 581 4.043561 TGGGCAAAAGGAGGAGTGTATAAA 59.956 41.667 0.00 0.00 0.00 1.40
566 582 3.589735 TGGGCAAAAGGAGGAGTGTATAA 59.410 43.478 0.00 0.00 0.00 0.98
568 584 1.992557 TGGGCAAAAGGAGGAGTGTAT 59.007 47.619 0.00 0.00 0.00 2.29
572 598 2.702270 AAATGGGCAAAAGGAGGAGT 57.298 45.000 0.00 0.00 0.00 3.85
610 636 0.179089 CCTGGCTGAATCAGAGGACG 60.179 60.000 15.38 0.00 30.00 4.79
611 637 1.134551 GTCCTGGCTGAATCAGAGGAC 60.135 57.143 25.61 25.61 43.34 3.85
612 638 1.198713 GTCCTGGCTGAATCAGAGGA 58.801 55.000 15.38 14.89 33.80 3.71
613 639 0.907486 TGTCCTGGCTGAATCAGAGG 59.093 55.000 15.38 12.71 34.36 3.69
743 776 1.853114 GAGACGTCACTCTGTCGCCA 61.853 60.000 19.50 0.00 40.05 5.69
828 864 4.335647 AGGTTGCCGTGCAGGAGG 62.336 66.667 8.24 2.99 45.00 4.30
1168 1208 0.747255 CTGTAGATGACCTCCACCCG 59.253 60.000 0.00 0.00 0.00 5.28
1292 1332 1.461091 GGTGTCACTGTCGTCCCTGA 61.461 60.000 2.35 0.00 0.00 3.86
1295 1335 0.034896 ATTGGTGTCACTGTCGTCCC 59.965 55.000 2.35 0.00 0.00 4.46
1296 1336 1.148310 CATTGGTGTCACTGTCGTCC 58.852 55.000 2.35 0.00 0.00 4.79
1297 1337 1.792949 GTCATTGGTGTCACTGTCGTC 59.207 52.381 2.35 0.00 0.00 4.20
1298 1338 1.865865 GTCATTGGTGTCACTGTCGT 58.134 50.000 2.35 0.00 0.00 4.34
1299 1339 0.784178 CGTCATTGGTGTCACTGTCG 59.216 55.000 2.35 0.00 31.86 4.35
1301 1341 1.138069 TGTCGTCATTGGTGTCACTGT 59.862 47.619 2.35 0.00 0.00 3.55
1302 1342 1.794701 CTGTCGTCATTGGTGTCACTG 59.205 52.381 2.35 0.00 0.00 3.66
1304 1344 1.526887 CACTGTCGTCATTGGTGTCAC 59.473 52.381 0.00 0.00 0.00 3.67
1307 1347 1.138069 TGTCACTGTCGTCATTGGTGT 59.862 47.619 0.66 0.00 0.00 4.16
1309 1349 1.540363 GGTGTCACTGTCGTCATTGGT 60.540 52.381 2.35 0.00 0.00 3.67
1310 1350 1.148310 GGTGTCACTGTCGTCATTGG 58.852 55.000 2.35 0.00 0.00 3.16
1312 1352 1.540363 GGTGGTGTCACTGTCGTCATT 60.540 52.381 2.35 0.00 43.17 2.57
1313 1353 0.033504 GGTGGTGTCACTGTCGTCAT 59.966 55.000 2.35 0.00 43.17 3.06
1314 1354 1.440060 GGTGGTGTCACTGTCGTCA 59.560 57.895 2.35 0.00 43.17 4.35
1489 1529 0.037697 TCGACCGATCAGGGTTGTTG 60.038 55.000 6.85 0.00 46.96 3.33
1493 1533 2.356780 GGGTCGACCGATCAGGGTT 61.357 63.158 27.68 0.00 46.96 4.11
1527 1567 2.500504 ACGGTTAGAACCCTTGATCCTC 59.499 50.000 5.85 0.00 46.53 3.71
1540 1580 1.776662 AGCCTGATAGCACGGTTAGA 58.223 50.000 0.00 0.00 34.23 2.10
1654 1694 7.397476 TGACCACATGATACTAAGAAGAGAGTT 59.603 37.037 0.00 0.00 0.00 3.01
1715 1755 3.614870 GCAGTTGGATTTTGCCGAAGATT 60.615 43.478 0.00 0.00 31.79 2.40
1717 1757 1.269448 GCAGTTGGATTTTGCCGAAGA 59.731 47.619 0.00 0.00 31.79 2.87
1719 1759 1.000385 CAGCAGTTGGATTTTGCCGAA 60.000 47.619 0.00 0.00 38.58 4.30
1766 1806 2.912956 TGCCCTCTGAATGAAACCTACT 59.087 45.455 0.00 0.00 0.00 2.57
1767 1807 3.350219 TGCCCTCTGAATGAAACCTAC 57.650 47.619 0.00 0.00 0.00 3.18
1769 1809 2.978156 TTGCCCTCTGAATGAAACCT 57.022 45.000 0.00 0.00 0.00 3.50
1793 1838 6.183360 GGCTAAGCATTCAATTCCAGGTTAAT 60.183 38.462 0.00 0.00 0.00 1.40
1795 1840 4.644685 GGCTAAGCATTCAATTCCAGGTTA 59.355 41.667 0.00 0.00 0.00 2.85
1803 1848 2.743553 AGCCTGGCTAAGCATTCAATT 58.256 42.857 21.98 0.00 36.99 2.32
1845 1891 4.130857 TGATCTCGTAAACCAAAAGCACA 58.869 39.130 0.00 0.00 0.00 4.57
1849 1895 7.464710 GCACTATCTGATCTCGTAAACCAAAAG 60.465 40.741 0.00 0.00 0.00 2.27
1861 1907 3.302365 GCAGAGGCACTATCTGATCTC 57.698 52.381 7.13 0.00 45.80 2.75
1885 1931 8.486383 CAAAATTATCATTTCACAGCACGAAAA 58.514 29.630 0.00 0.00 36.06 2.29
1889 1935 6.932901 ACAAAATTATCATTTCACAGCACG 57.067 33.333 0.00 0.00 30.80 5.34
1918 1964 8.121305 TGGCAAATACAACAAGATGATTAACT 57.879 30.769 0.00 0.00 0.00 2.24
1970 2021 2.754946 ATGCTTGCACCCAAATGAAG 57.245 45.000 0.00 0.00 0.00 3.02
1971 2022 5.010922 GGATATATGCTTGCACCCAAATGAA 59.989 40.000 0.00 0.00 0.00 2.57
1972 2023 4.523943 GGATATATGCTTGCACCCAAATGA 59.476 41.667 0.00 0.00 0.00 2.57
1973 2024 4.525487 AGGATATATGCTTGCACCCAAATG 59.475 41.667 0.04 0.00 0.00 2.32
1974 2025 4.744237 AGGATATATGCTTGCACCCAAAT 58.256 39.130 0.04 0.00 0.00 2.32
1975 2026 4.141181 AGAGGATATATGCTTGCACCCAAA 60.141 41.667 8.28 0.00 0.00 3.28
1976 2027 3.395607 AGAGGATATATGCTTGCACCCAA 59.604 43.478 8.28 0.00 0.00 4.12
1977 2028 2.981784 AGAGGATATATGCTTGCACCCA 59.018 45.455 8.28 0.00 0.00 4.51
1978 2029 3.710209 AGAGGATATATGCTTGCACCC 57.290 47.619 8.28 0.00 0.00 4.61
2012 2063 5.009410 GCTCTTGCCATGCTCAACTTATTAT 59.991 40.000 0.00 0.00 0.00 1.28
2045 2096 4.713814 TGATCAATAGAGCAGTCTGAACCT 59.286 41.667 3.32 0.00 34.77 3.50
2046 2097 5.016051 TGATCAATAGAGCAGTCTGAACC 57.984 43.478 3.32 0.00 34.77 3.62
2047 2098 7.551035 AATTGATCAATAGAGCAGTCTGAAC 57.449 36.000 21.00 0.00 41.81 3.18
2048 2099 9.842775 AATAATTGATCAATAGAGCAGTCTGAA 57.157 29.630 21.00 0.00 41.81 3.02
2080 2131 9.569122 AGTACTTTTTAGTGGTGTGTATTTGAT 57.431 29.630 0.00 0.00 0.00 2.57
2081 2132 8.832521 CAGTACTTTTTAGTGGTGTGTATTTGA 58.167 33.333 0.00 0.00 0.00 2.69
2082 2133 7.589954 GCAGTACTTTTTAGTGGTGTGTATTTG 59.410 37.037 0.00 0.00 0.00 2.32
2083 2134 7.519328 CGCAGTACTTTTTAGTGGTGTGTATTT 60.519 37.037 0.00 0.00 0.00 1.40
2084 2135 6.073440 CGCAGTACTTTTTAGTGGTGTGTATT 60.073 38.462 0.00 0.00 0.00 1.89
2085 2136 5.407387 CGCAGTACTTTTTAGTGGTGTGTAT 59.593 40.000 0.00 0.00 0.00 2.29
2086 2137 4.746115 CGCAGTACTTTTTAGTGGTGTGTA 59.254 41.667 0.00 0.00 0.00 2.90
2087 2138 3.558418 CGCAGTACTTTTTAGTGGTGTGT 59.442 43.478 0.00 0.00 0.00 3.72
2088 2139 3.805422 TCGCAGTACTTTTTAGTGGTGTG 59.195 43.478 0.00 0.00 0.00 3.82
2089 2140 3.805971 GTCGCAGTACTTTTTAGTGGTGT 59.194 43.478 0.00 0.00 0.00 4.16
2090 2141 4.056050 AGTCGCAGTACTTTTTAGTGGTG 58.944 43.478 0.00 0.00 0.00 4.17
2091 2142 4.332428 AGTCGCAGTACTTTTTAGTGGT 57.668 40.909 0.00 0.00 0.00 4.16
2092 2143 5.440685 CAAAGTCGCAGTACTTTTTAGTGG 58.559 41.667 0.00 0.00 45.20 4.00
2093 2144 4.904154 GCAAAGTCGCAGTACTTTTTAGTG 59.096 41.667 0.00 0.00 45.20 2.74
2094 2145 4.814771 AGCAAAGTCGCAGTACTTTTTAGT 59.185 37.500 0.00 0.00 45.20 2.24
2095 2146 5.344207 AGCAAAGTCGCAGTACTTTTTAG 57.656 39.130 0.00 0.00 45.20 1.85
2096 2147 5.987347 ACTAGCAAAGTCGCAGTACTTTTTA 59.013 36.000 0.00 3.19 45.20 1.52
2097 2148 4.814771 ACTAGCAAAGTCGCAGTACTTTTT 59.185 37.500 0.00 2.39 45.20 1.94
2098 2149 4.377897 ACTAGCAAAGTCGCAGTACTTTT 58.622 39.130 0.00 0.00 45.20 2.27
2100 2151 3.662247 ACTAGCAAAGTCGCAGTACTT 57.338 42.857 0.00 0.00 41.46 2.24
2101 2152 3.662247 AACTAGCAAAGTCGCAGTACT 57.338 42.857 0.00 0.00 37.50 2.73
2102 2153 4.232221 TGTAACTAGCAAAGTCGCAGTAC 58.768 43.478 0.00 0.00 37.50 2.73
2103 2154 4.508461 TGTAACTAGCAAAGTCGCAGTA 57.492 40.909 0.00 0.00 37.50 2.74
2104 2155 3.380479 TGTAACTAGCAAAGTCGCAGT 57.620 42.857 0.00 0.00 37.50 4.40
2105 2156 3.987868 TCTTGTAACTAGCAAAGTCGCAG 59.012 43.478 0.00 0.00 37.50 5.18
2106 2157 3.739300 GTCTTGTAACTAGCAAAGTCGCA 59.261 43.478 0.00 0.00 37.50 5.10
2107 2158 3.739300 TGTCTTGTAACTAGCAAAGTCGC 59.261 43.478 0.00 0.00 37.50 5.19
2108 2159 5.900339 TTGTCTTGTAACTAGCAAAGTCG 57.100 39.130 0.00 0.00 37.50 4.18
2109 2160 7.247929 AGTTTGTCTTGTAACTAGCAAAGTC 57.752 36.000 0.00 0.00 37.50 3.01
2110 2161 8.366671 CTAGTTTGTCTTGTAACTAGCAAAGT 57.633 34.615 8.55 9.89 43.81 2.66
2183 4611 3.864243 TCTGTACACCAAGTTCGTTTGT 58.136 40.909 0.00 0.00 0.00 2.83
2212 4640 3.162666 TCGGTCTCTCAACATAACCAGT 58.837 45.455 0.00 0.00 0.00 4.00
2313 4743 8.490355 GTCTTTTGATTTGGAAACTAATGCTTG 58.510 33.333 0.00 0.00 35.89 4.01
2391 4821 4.219507 TGCCCACACAAAAGTTATACATGG 59.780 41.667 0.00 0.00 0.00 3.66
2393 4823 5.624281 GCATGCCCACACAAAAGTTATACAT 60.624 40.000 6.36 0.00 0.00 2.29
2413 4843 4.610945 ACTTTTGAAACGAAGGAAGCATG 58.389 39.130 0.00 0.00 0.00 4.06
2457 4914 4.046938 TCTAATCGACCTCACATGAAGC 57.953 45.455 0.00 0.00 0.00 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.